<s>
GENESIS	B-Application
(	O
The	O
General	O
Neural	O
Simulation	O
System	O
)	O
is	O
a	O
simulation	O
environment	O
for	O
constructing	O
realistic	O
models	O
of	O
neurobiological	O
systems	O
at	O
many	O
levels	O
of	O
scale	O
including	O
:	O
sub-cellular	O
processes	O
,	O
individual	O
neurons	O
,	O
networks	B-Architecture
of	I-Architecture
neurons	I-Architecture
,	O
and	O
neuronal	O
systems	O
.	O
</s>
<s>
GENESIS	B-Application
is	O
intended	O
to	O
quantify	O
the	O
physical	O
framework	O
of	O
the	O
nervous	O
system	O
in	O
a	O
way	O
that	O
allows	O
for	O
easy	O
understanding	O
of	O
the	O
physical	O
structure	O
of	O
the	O
nerves	O
in	O
question	O
.	O
</s>
<s>
“	O
At	O
present	O
only	O
GENESIS	B-Application
allows	O
parallelized	O
modeling	O
of	O
single	O
neurons	O
and	O
networks	O
on	O
multiple-instruction-multiple-data	O
parallel	O
computers.	O
”	O
Development	O
of	O
GENESIS	B-Application
software	O
spread	O
from	O
its	O
home	O
at	O
Caltech	O
to	O
labs	O
at	O
the	O
University	O
of	O
Texas	O
at	O
San	O
Antonio	O
,	O
the	O
University	O
of	O
Antwerp	O
,	O
the	O
National	O
Centre	O
for	O
Biological	O
Sciences	O
in	O
Bangalore	O
,	O
the	O
University	O
of	O
Colorado	O
,	O
the	O
Pittsburgh	O
Supercomputing	O
Center	O
,	O
the	O
San	O
Diego	O
Supercomputer	O
Center	O
,	O
and	O
Emory	O
University	O
.	O
</s>
<s>
GENESIS	B-Application
works	O
by	O
creating	O
simulation	O
environments	O
for	O
constructing	O
models	O
of	O
neurons	O
or	O
neural	B-Architecture
systems	I-Architecture
.	O
</s>
<s>
To	O
understand	O
neural	B-Architecture
networks	I-Architecture
,	O
it	O
is	O
necessary	O
to	O
understand	O
the	O
ways	O
in	O
which	O
one	O
neuron	O
communicates	O
with	O
another	O
through	O
synaptic	O
connections	O
and	O
the	O
process	O
called	O
synaptic	O
transmission	O
"	O
.	O
</s>
<s>
The	O
two	O
important	O
regions	O
of	O
a	O
neuron	O
are	O
the	O
dendrite	O
and	O
the	O
axon	B-Algorithm
.	O
</s>
<s>
The	O
axon	B-Algorithm
is	O
a	O
key	O
component	O
of	O
nerve	O
cells	O
over	O
which	O
information	O
is	O
transmitted	O
from	O
one	O
part	O
of	O
the	O
neuron	O
(	O
e.g.	O
,	O
the	O
cell	O
body	O
)	O
to	O
the	O
terminal	O
regions	O
of	O
the	O
neuron	O
"	O
.	O
</s>
<s>
The	O
third	O
important	O
piece	O
of	O
a	O
neuron	O
is	O
the	O
synapse	B-Application
.	O
</s>
<s>
"	O
The	O
synapse	B-Application
is	O
the	O
terminal	O
region	O
of	O
the	O
axon	B-Algorithm
this	O
is	O
where	O
one	O
neuron	O
forms	O
a	O
connection	O
with	O
another	O
and	O
conveys	O
information	O
through	O
the	O
process	O
of	O
synaptic	O
transmission	O
"	O
.	O
</s>
<s>
Neural	B-Architecture
networks	I-Architecture
like	O
the	O
ones	O
simulated	O
with	O
GENESIS	B-Application
software	O
can	O
quickly	O
become	O
highly	O
complex	O
and	O
difficult	O
to	O
understand	O
.	O
</s>
<s>
GENESIS	B-Application
endeavors	O
to	O
simulate	O
neural	B-Architecture
systems	I-Architecture
as	O
they	O
are	O
found	O
in	O
nature	O
.	O
</s>
<s>
GENESIS	B-Application
was	O
developed	O
by	O
Dr.	O
James	O
M	O
.	O
Bower	O
,	O
in	O
the	O
Caltech	O
laboratory	O
,	O
and	O
first	O
released	O
to	O
the	O
public	O
in	O
1988	O
in	O
association	O
with	O
the	O
first	O
Methods	O
in	O
Computational	O
Neuroscience	O
Course	O
at	O
the	O
Marine	O
Biological	O
Laboratory	O
in	O
Woods	O
Hole	O
,	O
MA	O
.	O
</s>
<s>
Full	O
source	O
code	O
for	O
the	O
software	O
was	O
released	O
in	O
the	O
same	O
year	O
under	O
an	O
open	B-Application
software	I-Application
model	O
for	O
development	O
.	O
</s>
<s>
P-GENESIS	O
,	O
a	O
parallel	O
version	O
of	O
GENESIS	B-Application
,	O
was	O
first	O
run	O
in	O
1990	O
on	O
the	O
Intel	O
Delta	O
,	O
which	O
was	O
the	O
prototype	O
for	O
the	O
Intel	B-Device
Paragon	I-Device
family	O
of	O
massively	O
parallel	O
supercomputers	O
.	O
</s>
<s>
GENESIS	B-Application
is	O
useful	O
in	O
creating	O
a	O
simulation	O
environment	O
for	O
constructing	O
models	O
of	O
neurobiological	O
systems	O
such	O
as	O
:	O
</s>
<s>
The	O
GENESIS	B-Application
system	O
is	O
complicated	O
,	O
but	O
relatively	O
easy	O
to	O
use	O
.	O
</s>
<s>
An	O
individual	O
can	O
input	O
commands	O
through	O
one	O
of	O
three	O
ways	O
:	O
script	O
files	O
,	O
graphical	O
user	O
interface	O
,	O
or	O
the	O
GENESIS	B-Application
command	O
shell	O
.	O
</s>
<s>
"	O
The	O
Script	O
Language	O
Interpreter	O
processes	O
commands	O
entered	O
through	O
the	O
keyboard	O
,	O
script	O
files	O
,	O
or	O
the	O
graphical	O
user	O
interface	O
,	O
and	O
passes	O
them	O
to	O
the	O
GENESIS	B-Application
simulation	O
engine	O
.	O
</s>
<s>
Below	O
is	O
a	O
graphical	O
representation	O
of	O
the	O
user	O
input	O
process	O
and	O
a	O
sample	O
GENESIS	B-Application
output	O
.	O
</s>
<s>
Most	O
current	O
applications	O
for	O
GENESIS	B-Application
involve	O
realistic	O
simulations	O
of	O
biological	O
systems	O
.	O
</s>
<s>
GENESIS	B-Application
can	O
be	O
used	O
in	O
combination	O
with	O
Yale	O
University	O
’s	O
software	O
called	O
NEURON	O
as	O
a	O
means	O
for	O
scientists	O
to	O
collaborate	O
to	O
construct	O
a	O
physical	O
description	O
of	O
the	O
nervous	O
system	O
.	O
</s>
<s>
The	O
GENESIS	B-Application
software	O
can	O
also	O
be	O
used	O
with	O
Kinetikit	O
in	O
the	O
modeling	O
of	O
signal	O
transduction	O
pathways	O
.	O
</s>
<s>
GENESIS	B-Application
has	O
been	O
used	O
in	O
many	O
studies	O
.	O
</s>
<s>
These	O
studies	O
used	O
GENESIS	B-Application
to	O
simulate	O
Purkinje	O
cells	O
and	O
could	O
be	O
useful	O
for	O
the	O
planning	O
and	O
development	O
of	O
later	O
experiments	O
using	O
the	O
GENESIS	B-Application
software	O
.	O
</s>
<s>
For	O
example	O
,	O
St.	O
Jude	O
Medical	O
in	O
Europe	O
has	O
developed	O
an	O
implanted	O
GENESIS	B-Application
device	O
.	O
</s>
